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Break the monolithic process_gencode_data into 6 independently testable static methods (parse_raw_gtf, parse_gtf_annotations, strip_gene_id_version, filter_protein_coding_genes, add_length_column, process_single_gene) and fix the chromosome filter to handle the 'chr' prefix in standard GTF files. Add unit tests for each extracted method plus integration tests using a sample GENCODE GTF (OPRK1 / ENSG00000082556). Move config.json to repo root. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
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Codecov Report❌ Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## master #35 +/- ##
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- Coverage 88.79% 82.73% -6.06%
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Files 6 10 +4
Lines 348 695 +347
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+ Hits 309 575 +266
- Misses 39 120 +81 ☔ View full report in Codecov by Sentry. 🚀 New features to boost your workflow:
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Context
There was a large-scale update of the repository with help of agentic tool Calude. This left a handful of small issues. At this point the code runs. This can be considered as as baseline for further more meaningful updates.
Contents
README.mdfile.Warnings
Dynamic libraries are hard-coded in packages that are relying on cairo. This must be a temporary update. Should be refactored later.